Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008398.1 Hibiscus syriacus cultivar Beakdansim tig00111167_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 50278
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:5472 original size:31 final size:31
Alignment explanation
Indices: 5436--5518 Score: 103
Period size: 32 Copynumber: 2.6 Consensus size: 31
5426 TAACTTTCAA
*
5436 TACAAAATGGTCATTAAATTTATCGAACTGT
1 TACAAAATGGTCATTAAATTTATCGAAATGT
* *
5467 TACAAAATGATTATTAAATTTTATCGAAATGT
1 TACAAAATGGTCATTAAA-TTTATCGAAATGT
* *
5499 TGCAAAATAGTCATTGAAAT
1 TACAAAATGGTCATT-AAAT
5519 ATCAAATTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
31 16 0.37
32 24 0.56
33 3 0.07
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.36
Consensus pattern (31 bp):
TACAAAATGGTCATTAAATTTATCGAAATGT
Found at i:15828 original size:15 final size:16
Alignment explanation
Indices: 15808--15840 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
15798 TCGATTTAAG
*
15808 TATCG-ATTTTATTTT
1 TATCGAATTTTATATT
15823 TATCGAATTTTATATT
1 TATCGAATTTTATATT
15839 TA
1 TA
15841 AGTTTAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.27, C:0.06, G:0.06, T:0.61
Consensus pattern (16 bp):
TATCGAATTTTATATT
Found at i:25103 original size:19 final size:19
Alignment explanation
Indices: 25079--25116 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
25069 GGGAGAAGAA
25079 TAAGTGTTAAATGTTTTAC
1 TAAGTGTTAAATGTTTTAC
25098 TAAGTGTTAAATGTTTTAC
1 TAAGTGTTAAATGTTTTAC
25117 ATGATAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.05, G:0.16, T:0.47
Consensus pattern (19 bp):
TAAGTGTTAAATGTTTTAC
Found at i:26533 original size:35 final size:36
Alignment explanation
Indices: 26487--26572 Score: 95
Period size: 35 Copynumber: 2.4 Consensus size: 36
26477 ATTCTAAATG
* *
26487 TTTACATTTATCA-AACATTTCACTGTTATCAGAT-A
1 TTTACAATTATCAGAACATTT-ACAGTTATCAGATGA
** *
26522 TTTACAATTATCAGATGATTTACAGTTATCAGATGT
1 TTTACAATTATCAGAACATTTACAGTTATCAGATGA
*
26558 TTTTCAATTATCAGA
1 TTTACAATTATCAGA
26573 TGTAGATTAA
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
35 24 0.56
36 19 0.44
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.43
Consensus pattern (36 bp):
TTTACAATTATCAGAACATTTACAGTTATCAGATGA
Found at i:26575 original size:18 final size:18
Alignment explanation
Indices: 26512--26574 Score: 92
Period size: 18 Copynumber: 3.6 Consensus size: 18
26502 CATTTCACTG
26512 TTATCAGAT-ATTTACAA
1 TTATCAGATGATTTACAA
*
26529 TTATCAGATGATTTACAG
1 TTATCAGATGATTTACAA
* *
26547 TTATCAGATGTTTTTCAA
1 TTATCAGATGATTTACAA
26565 TTATCAGATG
1 TTATCAGATG
26575 TAGATTAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
17 9 0.22
18 32 0.78
ACGTcount: A:0.33, C:0.11, G:0.13, T:0.43
Consensus pattern (18 bp):
TTATCAGATGATTTACAA
Found at i:33493 original size:21 final size:22
Alignment explanation
Indices: 33444--33513 Score: 74
Period size: 22 Copynumber: 3.3 Consensus size: 22
33434 AATAACCAAT
* *
33444 AAATTCGCAACGCGAA-CT-CC
1 AAATTCGCAACACGAATTTCCC
* *
33464 AATTTCGCAACAC-AATTTCCT
1 AAATTCGCAACACGAATTTCCC
*
33485 AAATTCGCAACGCGAATTTCCC
1 AAATTCGCAACACGAATTTCCC
33507 AAATTCG
1 AAATTCG
33514 TAACTGAGTT
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
19 2 0.05
20 12 0.30
21 12 0.30
22 14 0.35
ACGTcount: A:0.34, C:0.30, G:0.11, T:0.24
Consensus pattern (22 bp):
AAATTCGCAACACGAATTTCCC
Found at i:33502 original size:22 final size:22
Alignment explanation
Indices: 33443--33545 Score: 92
Period size: 21 Copynumber: 4.9 Consensus size: 22
33433 AAATAACCAA
*
33443 TAAATTCGCAACGCGAA-CTCC
1 TAAATTCGCAACGCGAATTTCC
* *
33464 -AATTTCGCAACAC-AATTTCC
1 TAAATTCGCAACGCGAATTTCC
33484 TAAATTCGCAACGCGAATTTCC
1 TAAATTCGCAACGCGAATTTCC
* * * *
33506 CAAATTCGTAAC-TGAGTTT-C
1 TAAATTCGCAACGCGAATTTCC
33526 TGAAA-TCGCAACGCGAATTT
1 T-AAATTCGCAACGCGAATTT
33546 GCACATAAGT
Statistics
Matches: 64, Mismatches: 13, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
19 2 0.03
20 21 0.33
21 24 0.38
22 17 0.27
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.27
Consensus pattern (22 bp):
TAAATTCGCAACGCGAATTTCC
Found at i:33750 original size:21 final size:22
Alignment explanation
Indices: 33726--33772 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
33716 CTCTCTACGA
*
33726 CGACATCCGTCCCCATCTCC-G
1 CGACATCCGTCCCCATATCCGG
33747 CGACATCCGTCCCCATATCCGG
1 CGACATCCGTCCCCATATCCGG
33769 CGAC
1 CGAC
33773 CCCCTTATCT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 19 0.79
22 5 0.21
ACGTcount: A:0.17, C:0.49, G:0.17, T:0.17
Consensus pattern (22 bp):
CGACATCCGTCCCCATATCCGG
Found at i:34132 original size:20 final size:20
Alignment explanation
Indices: 34109--34147 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
34099 TTTGAAATTT
34109 AAATTCGCAACACGAAAATG
1 AAATTCGCAACACGAAAATG
34129 AAATTCGCAACACGAAAAT
1 AAATTCGCAACACGAAAAT
34148 CGCAACGCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.51, C:0.21, G:0.13, T:0.15
Consensus pattern (20 bp):
AAATTCGCAACACGAAAATG
Found at i:34177 original size:20 final size:21
Alignment explanation
Indices: 34157--34207 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
34147 TCGCAACGCG
*
34157 ATTTTAGTTTTCGCGTTGCGA
1 ATTTAAGTTTTCGCGTTGCGA
* *
34178 ATTTCA-TTTTCGTGTTGCGA
1 ATTTAAGTTTTCGCGTTGCGA
34198 ATTTAAGTTT
1 ATTTAAGTTT
34208 CAAAAACTAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 18 0.69
21 8 0.31
ACGTcount: A:0.18, C:0.12, G:0.20, T:0.51
Consensus pattern (21 bp):
ATTTAAGTTTTCGCGTTGCGA
Found at i:35749 original size:42 final size:42
Alignment explanation
Indices: 35689--35787 Score: 162
Period size: 42 Copynumber: 2.4 Consensus size: 42
35679 CCCCCTACTT
* * *
35689 CGAGAGCCATCACCTGATCGAGCCGATTCTACAGCTCGACAC
1 CGAGAGCCATCACCTGATCGAGCCGATTATACACCTAGACAC
*
35731 CGAGAGCCATCACTTGATCGAGCCGATTATACACCTAGACAC
1 CGAGAGCCATCACCTGATCGAGCCGATTATACACCTAGACAC
35773 CGAGAGCCATCACCT
1 CGAGAGCCATCACCT
35788 ATTCCATCAC
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.28, C:0.34, G:0.20, T:0.17
Consensus pattern (42 bp):
CGAGAGCCATCACCTGATCGAGCCGATTATACACCTAGACAC
Found at i:35929 original size:21 final size:21
Alignment explanation
Indices: 35902--35951 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
35892 GTTAGGGGAG
*
35902 TTACGTGATGAGGTCAGTGCT
1 TTACGTGATGAGGTCAGTACT
* *
35923 TTGCGTGATGAGGTCGGTACT
1 TTACGTGATGAGGTCAGTACT
35944 TTACGTGA
1 TTACGTGA
35952 CGACAATGGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.18, C:0.14, G:0.34, T:0.34
Consensus pattern (21 bp):
TTACGTGATGAGGTCAGTACT
Found at i:36383 original size:21 final size:21
Alignment explanation
Indices: 36357--36468 Score: 100
Period size: 21 Copynumber: 5.3 Consensus size: 21
36347 GAAGAAGCCC
* *
36357 GATCCACCTGCCATTGTTCAG
1 GATCCACCTCCCATCGTTCAG
*
36378 GATCCACCTCCCATTGTTCAG
1 GATCCACCTCCCATCGTTCAG
* * ** *
36399 GATTCATCTGTCATCGTTCAA
1 GATCCACCTCCCATCGTTCAG
* * *
36420 GAGGCC-CCTCTCATCGTTCAA
1 GA-TCCACCTCCCATCGTTCAG
*
36441 GATCCACCTCCCACCGTTCAG
1 GATCCACCTCCCATCGTTCAG
36462 GATCCAC
1 GATCCAC
36469 ATGGCATACT
Statistics
Matches: 74, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
20 2 0.03
21 71 0.96
22 1 0.01
ACGTcount: A:0.21, C:0.37, G:0.16, T:0.27
Consensus pattern (21 bp):
GATCCACCTCCCATCGTTCAG
Found at i:38014 original size:20 final size:20
Alignment explanation
Indices: 37989--38056 Score: 93
Period size: 20 Copynumber: 3.4 Consensus size: 20
37979 GCGATTTTTT
*
37989 ATTTTCGCG-TGTCAAATTTG
1 ATTTTCGCGTTG-CGAATTTG
*
38009 ATTTTCGTGTTGCGAATTTG
1 ATTTTCGCGTTGCGAATTTG
38029 ATTTTCGCGTTGCGAATTTG
1 ATTTTCGCGTTGCGAATTTG
*
38049 ACTTTCGC
1 ATTTTCGC
38057 AATAATCGCA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
20 41 0.95
21 2 0.05
ACGTcount: A:0.16, C:0.16, G:0.22, T:0.46
Consensus pattern (20 bp):
ATTTTCGCGTTGCGAATTTG
Found at i:40553 original size:24 final size:23
Alignment explanation
Indices: 40515--40568 Score: 81
Period size: 24 Copynumber: 2.3 Consensus size: 23
40505 TCAAAACATC
40515 ATCAAATCCGAGTATTGACCAAG
1 ATCAAATCCGAGTATTGACCAAG
* *
40538 ATCAAAGTCCGGGTATTGACCAAT
1 ATCAAA-TCCGAGTATTGACCAAG
40562 ATCAAAT
1 ATCAAAT
40569 TTCGAATACT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 7 0.25
24 21 0.75
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (23 bp):
ATCAAATCCGAGTATTGACCAAG
Found at i:41608 original size:61 final size:60
Alignment explanation
Indices: 41528--41643 Score: 155
Period size: 61 Copynumber: 1.9 Consensus size: 60
41518 TTGCGAAAAG
41528 AATTCGCGTTACGAATTCAGAAA-TCCAGTTGCGAATTTG-AAATTCCGTGTTGCGAATTTGA
1 AATTCGCGTTACGAATTCAGAAACT-CAGTTGCGAATTTGAAAATT--GTGTTGCGAATTTGA
* * * *
41589 AATTTGCGTTGCGATTTCAGAAACTGAGTTGCGAATTTGAAAATTGTGTTGCGAA
1 AATTCGCGTTACGAATTCAGAAACTCAGTTGCGAATTTGAAAATTGTGTTGCGAA
41644 ATTGGAGTTC
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
60 10 0.20
61 33 0.67
62 6 0.12
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.34
Consensus pattern (60 bp):
AATTCGCGTTACGAATTCAGAAACTCAGTTGCGAATTTGAAAATTGTGTTGCGAATTTGA
Found at i:41646 original size:21 final size:20
Alignment explanation
Indices: 41555--41643 Score: 92
Period size: 20 Copynumber: 4.4 Consensus size: 20
41545 CAGAAATCCA
41555 GTTGCGAATTTG-AAATTCCGT
1 GTTGCGAATTTGAAAATT--GT
* *
41576 GTTGCGAATTTGAAATTTGC
1 GTTGCGAATTTGAAAATTGT
* * *
41596 GTTGCG-ATTTCAGAAACTGA
1 GTTGCGAATTTGA-AAATTGT
41616 GTTGCGAATTTGAAAATTGT
1 GTTGCGAATTTGAAAATTGT
41636 GTTGCGAA
1 GTTGCGAA
41644 ATTGGAGTTC
Statistics
Matches: 56, Mismatches: 9, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
19 5 0.09
20 30 0.54
21 17 0.30
22 4 0.07
ACGTcount: A:0.27, C:0.11, G:0.26, T:0.36
Consensus pattern (20 bp):
GTTGCGAATTTGAAAATTGT
Found at i:42341 original size:28 final size:29
Alignment explanation
Indices: 42308--42381 Score: 98
Period size: 28 Copynumber: 2.6 Consensus size: 29
42298 ATAATTTTTT
*
42308 TAATCATTAAAATTTTAAA-ATTTACAAA
1 TAATCATTAAAATTTTAAACAATTACAAA
*
42336 TAATCATTAAAATTTTTAAACAATTATAAA
1 TAATCATTAAAA-TTTTAAACAATTACAAA
*
42366 TAATCA-TCAAATTTTA
1 TAATCATTAAAATTTTA
42382 TCAACTATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
28 17 0.41
29 11 0.27
30 13 0.32
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (29 bp):
TAATCATTAAAATTTTAAACAATTACAAA
Found at i:42369 original size:30 final size:29
Alignment explanation
Indices: 42308--42380 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
42298 ATAATTTTTT
*
42308 TAATCATTAAAA-TTTTAAAATTTACAAA
1 TAATCATTAAAATTTTTAAAAATTACAAA
*
42336 TAATCATTAAAATTTTTAAACAATTATAAA
1 TAATCATTAAAATTTTTAAA-AATTACAAA
*
42366 TAATCA-TCAAATTTT
1 TAATCATTAAAATTTT
42381 ATCAACTATT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
28 12 0.30
29 15 0.38
30 13 0.32
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (29 bp):
TAATCATTAAAATTTTTAAAAATTACAAA
Found at i:48295 original size:17 final size:17
Alignment explanation
Indices: 48269--48307 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
48259 TAAAATTACA
*
48269 AAATTTCAGAAAATACG
1 AAATTACAGAAAATACG
48286 AAATTACAGAAAATACG
1 AAATTACAGAAAATACG
48303 AAATT
1 AAATT
48308 TTATATTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.56, C:0.10, G:0.10, T:0.23
Consensus pattern (17 bp):
AAATTACAGAAAATACG
Done.